:: Software ::
|DT-CWT-NLM: Dual-tree complex wavelet combined with non-local means for ASL fMRI denoising
Developer: Xiaoyun Liang, PhD
Dual-tree complex wavelet combined with
non-local means (DT-CWT-NLM) for Arterial-Spin-Labelling (ASL) fMRI denoising is a software toolbox that can
denoise MR images, especially ASL fMRI. The software is typically used as a pre-processing step,
reading, denoising and writing NIfTI format images. Variable denoising outcomes are possible by
changing certain parameters. The software can also be employed for denoising other MR image types,
such as diffusion MRI.
The method is described in the following paper:
Voxel-wise functional connectomics using arterial spin labeling fMRI: the role of denoising.
Xiaoyun Liang, Alan Connelly, Fernando Calamante, 2015. Brain connectivity.
DT-CWT-NLM is released under the GNU General Public License and is available for
download at NITRC.
iBrain, the iBrain Analysis Toolbox for SPM,
and the iBrain Laterality Toolbox
Principal developer: David Abbott, PhD
Co-developers: Richard Masterton, PhD; Tony Waites, PhD; Kaushik Bhaganagarapu; Gaby Pell, PhD; Matt Harvey; Gagan Sharma; Chris Tailby, PhD; Graeme Jackson, MD.
iBrain software comprises several easy-to-use
neuroimage processing and visualisation packages developed by David
Abbott PhD and his team. Please see the iBrain software page for more details.
|MRtrix: MR tractography including crossing fibres
Principal Developer: Donald Tournier, PhD
Co-developers: David Raffelt, PhD; Robert Smith, PhD; Ben Jeurissen, PhD
MRtrix provides a set of tools to perform diffusion-weighted MR
white-matter tractography in a manner robust to crossing fibres, using
constrained spherical deconvolution (CSD) and probabilistic streamlines.
MRtrix is released under the GNU General Public License. The stable 0.2 version is available for
download at NITRC. Documentation for this version
is available here. Note that this
version is no longer under active development and now only receives bug fix updates.
The new MRtrix3 release, which includes the latest developments,
is available on the MRtrix3 GitHub page, along with its
documentation. While this version isn't yet an official release, it is already very stable. However, note that it is
under active development, and as such subject to frequent changes.
|NFG: The 'Numerical Fibre Generator'
Developer: Tom Close
NFG is a collection of command-line tools that enable the generation of numerical fibre structures with a range of complexities spanning the levels expected of human white matter. Also included is a tool to simulate the diffusion-weighted MR (DW-MR) images that would arise from these structures under various imaging conditions. The primary use of the 'Numerical Fibre Generator' is to enable the testing of white-matter fibre tracking techniques based on DW-MRI.
All included tools are distributed under the GNU public licence (GPL)
and are available for download at NITRC
Principal developer: Kaushik Bhaganagarapu
Co-developer: David Abbott, PhD.
SOCK (Spatially Organized Component Klassifikator)
can be used to automatically identify a high proportion of the artifactual components arising in Independent Componenets Analysis (ICA) of fMRI. It is described in detail in the following manuscript:
Bhaganagarapu K, Jackson GD, Abbott DF. An automated method for identifying artifact in Independent Component Analysis of resting-state fMRI.
Frontiers in Human Neuroscience 7(343):1-16 (2013). (doi: 10.3389/fnhum.2013.00343).
SOCK can also be used as an automated pre-processing noise filter in fMRI analysis pilpelines, via the included batch_SOCK routine. Use of SOCK as a noise filter is
described in the following manuscript:
Bhaganagarapu K, Jackson GD, Abbott DF. De-noising with a SOCK can improve the performance of event-related ICA.
Frontiers in Neuroscience 8(285):1-9 (2014). (doi: 10.3389/fnins.2014.00285).
The SOCK software is written in Matlab and presently works well with MELODIC ICA software
(part of FSL from FMRIB).
SOCK software is released under
the GNU General Public License, and is now available for
download at NITRC.